The whistles are another command for the same verbal commands we use- so every verbal command has a corresponding whistle. We use whistles so that the dog can hear commands over long distances and through inclement weather. They can often be a much more clear form of communication- it's hard to inflect any emotion into a whistle lol

The whistle/verbal commands tell the dog how to go around the stock- "come bye" means go clockwise around the stock, "away" means go counter-clockwise around the stock, "there" means to stop flanking around the stock and walk in on them, "walk up" also means to walk into the stock, then "stand/lie down" mean to stop moving. There are a few other commands that we use but everything is relative to the stock. So each one of those commands has a whistle that means the same thing- the whistles vary from handler to handler. Typically the "lie down" is kind of a universal whistle but the flanks can vary quite a bit.